We present a deep neural net-based region of interest detection method (DNN ROI) for signal processing in the liquid argon time projection chambers of the Short-Baseline Neutrino (SBN) Program, SBND and ICARUS. DNN ROI addresses limitations of the traditional wire-by-wire thresholding algorithm by leveraging the full two-dimensional detector readout and cross-plane matching information. To account for detector performance variations, we explore training with augmented samples. We find that DNN ROI outperforms the traditional method in both low-level ROI identification performance and high-level reconstruction metrics for high-energy cosmic and accelerator neutrino interaction products, while also being more robust against detector variations, with or without sample augmentation.